Recombinant human brain-derived neurotrophic factor in acid undergoes a slow loss of tertiary structure as monitored by both near-UV circular dichroism and fluorescence, and appears to retain some secondary structure, as monitored by far-UV circular dichroism and Fourier transform infrared spectroscopy. This loss of tertiary structure parallels a decrease in the weight average molecular weight, from dimer to monomer, when examined using light scattering. Increasing the temperature accelerates this slow reaction. This process may be described most simply as N2 in equilibrium with 2D where N and D are the native and denatured forms of the protein, respectively. However, the acid denaturation strongly depends on the protein concentration, with higher concentration resulting in a lower rate and extent of denaturation. This suggests that the more complicated mechanism N2 in equilibrium with 2N in equilibrium with 2D more accurately describes the denaturation, where the dissociation into a native monomer is the rate-limiting step, and the conversion of N to D occurs relatively rapidly. Size-exclusion chromatography (at neutral pH) at several points during denaturation further demonstrated that the amount of tertiary structure remaining paralleled the dimer concentration and also that the monomer form was long-lived, remaining as monomer during the course of the chromatography. Size-exclusion chromatography and sedimentation velocity determination indicated that the acid-denatured form is a compact molecule. On the basis of the above data, the acid-denatured form may be considered to be a monomeric compact intermediate A state with no tertiary structure but considerable secondary structure.(ABSTRACT TRUNCATED AT 250 WORDS)